The same code works on Mac but not on Linux. Both systems are using msa_1.30.1 (link to msa).

Does anyone have any ideas about what is wrong?

Here is the code:

library(msa)
set.seed(1)
seqs <- replicate(10, paste(sample(c("A", "T", "G", "C"), 10, replace = TRUE), collapse = ""))
fasta_file <- "temp.fa"
writeLines(sprintf(">%s\n%s", seq_along(seqs), seqs), fasta_file)
msa(fasta_file, type = "dna")

On Mac I get this:

#> use default substitution matrix
#> CLUSTAL 2.1  
#> 
#> Call:
#>    msa(fasta_file, type = "dna")
#> 
#> MsaDNAMultipleAlignment with 10 rows and 17 columns
#>      aln 
#>  [1] ---ACGATAGGTT----
#>  [2] ------TTAGGCTGGC-
#>  [3] ---TTACGACGTT----
#>  [4] ----TACCAGCTTG---
#>  [5] TTGCCCTCAG-------
#>  [6] -GTTCCTTATT------
#>  [7] -------GGAAATTTTG
#>  [8] ------AGAAAATAAT-
#>  [9] ------TCGGACACAC-
#> [10] ----AGTCGAACTA---
#>  Con ----??T?AG??T?---

On Linux I get this:

#> use default substitution matrix
#> ERROR: Cannot open input file. No alignment!
#> Error in msaFun(inputSeqs = inputSeqs, cluster = cluster, gapOpening = gapOpening, : ClustalW finished with errors

On Linux I can run the following code without a problem (but notice the output is different than on the Mac):

> msa(seqs, type = "dna")
use default substitution matrix
CLUSTAL 2.1

Call:
   msa(seqs, type = "dna")

MsaDNAMultipleAlignment with 10 rows and 16 columns
     aln
 [1] ---ACGATAGGTT---
 [2] ------TTAGGCTGGC
 [3] ---TTACGACGTT---
 [4] ----TACCAGCTTG--
 [5] TTGCCCTCAG------
 [6] -GTTCCTTATT-----
 [7] ----GGAAATTTTG--
 [8] ---AGAAAATAAT---
 [9] --TCGGACACAC----
[10] AGTCGAACTA------
 Con ---???A?A???T---

Mac session info:

sessionInfo()
#> R version 4.2.3 (2023-03-15)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Ventura 13.4
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#> [1] msa_1.30.1          Biostrings_2.66.0   GenomeInfoDb_1.34.9
#> [4] XVector_0.38.0      IRanges_2.32.0      S4Vectors_0.36.2   
#> [7] BiocGenerics_0.44.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.11            rstudioapi_0.15.0      knitr_1.43            
#>  [4] magrittr_2.0.3         zlibbioc_1.44.0        R.cache_0.16.0        
#>  [7] rlang_1.1.2            fastmap_1.1.1          styler_1.10.2         
#> [10] tools_4.2.3            xfun_0.39              R.oo_1.26.0           
#> [13] cli_3.6.1              withr_2.5.2            htmltools_0.5.5       
#> [16] yaml_2.3.7             digest_0.6.31          lifecycle_1.0.4       
#> [19] crayon_1.5.2           GenomeInfoDbData_1.2.9 purrr_1.0.1           
#> [22] bitops_1.0-7           vctrs_0.6.5            R.utils_2.12.3        
#> [25] fs_1.6.2               RCurl_1.98-1.12        glue_1.6.2            
#> [28] evaluate_0.21          rmarkdown_2.23         reprex_2.0.2          
#> [31] compiler_4.2.3         R.methodsS3_1.8.2

Linux session info:

sessionInfo()
#> R version 4.2.2 Patched (2022-11-10 r83330)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.5 LTS
#>
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
#>
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8
#>  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C
#> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods   base
#>
#> other attached packages:
#> [1] msa_1.30.1          Biostrings_2.66.0   GenomeInfoDb_1.34.9 XVector_0.38.0
#> [5] IRanges_2.32.0      S4Vectors_0.36.1    BiocGenerics_0.44.0
#>
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.10            knitr_1.42             zlibbioc_1.44.0        rlang_1.1.0
#>  [5] fastmap_1.1.1          tools_4.2.2            xfun_0.38              cli_3.6.1
#>  [9] withr_2.5.0            htmltools_0.5.5        yaml_2.3.7             digest_0.6.31
#> [13] lifecycle_1.0.3        crayon_1.5.2           GenomeInfoDbData_1.2.9 fs_1.6.1
#> [17] bitops_1.0-7           RCurl_1.98-1.10        glue_1.6.2             evaluate_0.20
#> [21] rmarkdown_2.21         reprex_2.0.2           compiler_4.2.2